In the flywheel charging-control system, there exists the flywheel motorís nonlinearity, variable elements etc, which leads to the problem of parameter tuning of PID controller of its charging-control systemís revolving speed loop. In this study, I will introduce an optimizing way based on modified genetic algorithm for the flywheel charging-control system PID controller, which by means of simulation and performance index quantization to observe its optimizing performance and convergence characteristic, so that we can check the feasibility and effectiveness in the flywheel charging-control system. It turns out that tuning PID controller parameters based on modified genetic algorithm has a better rapidity and stability, which proves the feasibility of the modified genetic algorithm.